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Yorodumi- PDB-3cec: Crystal structure of a putative antidote protein of plasmid maint... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cec | ||||||
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Title | Crystal structure of a putative antidote protein of plasmid maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at 1.60 A resolution | ||||||
Components | Putative antidote protein of plasmid maintenance system | ||||||
Keywords | TRANSCRIPTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc punctiforme (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative antidote protein of plasmid maintenance system (ZP_00107635.1) from Nostoc punctiforme PCC 73102 at 1.60 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cec.cif.gz | 32.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cec.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cec_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 3cec_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 3cec_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 3cec_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3cec ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3cec | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11885.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00107635.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VWT6*PLUS |
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#2: Chemical | ChemComp-MRD / ( |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Sequence details | 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NANODROP, 40.0% 2-Methyl-2,4-pentanediol, 5.0% PEG 8000, 0.1M Sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97925, 0.97883 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→25.214 Å / Num. obs: 16808 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.415 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.26 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→25.214 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.676 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.078 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 2-METHYL-2,4-PENTANEDIOL AND POLYETHYLENE GLYCOL FROM CRYSTALLIZATION CONDITION ARE MODELED IN THIS STRUCTURE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.034 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25.214 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.639 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 24.138 Å / Origin y: 9.752 Å / Origin z: 38.517 Å
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